GapMind for catabolism of small carbon sources

 

trehalose catabolism in Sphingomonas koreensis DSMZ 15582

Best path

treF, MFS-glucose, glk

Also see fitness data for the top candidates

Rules

Overview: Trehalose degradation is based on MetaCyc pathways I via trehalose-6-phosphate hydrolase (link), II via cytoplasmic trehalase (link), III via trehalose-6-phosphate phosphorylase (link), IV via inverting trehalose phosphorylase (link), V via trehalose phosphorylase (link), VI via periplasmic trehalase (link), as well as trehalose degradation via 3-ketotrehalose (PMID:33657378).

74 steps (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase Ga0059261_0579 Ga0059261_1580
MFS-glucose glucose transporter, MFS superfamily Ga0059261_1891 Ga0059261_0767
glk glucokinase Ga0059261_0355 Ga0059261_1776
Alternative steps:
aglE trehalose ABC transporter, substrate-binding component AglE
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF trehalose ABC transporter, permease component 1 (AglF)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG trehalose ABC transporter, permease component 2 (AglG)
aglG' glucose ABC transporter, permease component 2 (AglG)
aglK trehalose ABC trehalose, ATPase component AglK Ga0059261_3668 Ga0059261_0562
aglK' glucose ABC transporter, ATPase component (AglK) Ga0059261_3668 Ga0059261_0562
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA Ga0059261_1646
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Ga0059261_0356 Ga0059261_1625
edd phosphogluconate dehydratase Ga0059261_0354 Ga0059261_4216
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU)
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) Ga0059261_3874 Ga0059261_1321
gnl gluconolactonase Ga0059261_1893
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) Ga0059261_3668 Ga0059261_3874
kguD 2-keto-6-phosphogluconate reductase Ga0059261_2669 Ga0059261_2264
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
klh 3-ketotrehalose hydrolase Ga0059261_0549
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit Ga0059261_0546
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB)
lacC periplasmic trehalose 3-dehydrogenase, LacC subunit
lpqY trehalose ABC transporter, substrate-binding lipoprotein component LpqY
malE2 trehalose ABC transporter, substrate-binding component MalE2
malF trehalose ABC transporter, permease component 1 (MalF)
malF1 trehalose ABC transporter, permease component 1
malG trehalose ABC transporter, permease component 2 (MalG)
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK Ga0059261_1321 Ga0059261_3874
malX trehalose ABC transporter, substrate-binding component MalX
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
mglA glucose ABC transporter, ATP-binding component (MglA) Ga0059261_2542 Ga0059261_3276
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Ga0059261_2456 Ga0059261_1954
pgmB beta-phosphoglucomutase
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB Ga0059261_1647
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) Ga0059261_1647
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter Ga0059261_1623
SWEET1 bidirectional sugar transporter SWEET1
thuE trehalose ABC transporter, substrate-binding component ThuE
thuF trehalose ABC transporter, permease component 1 (ThuF)
thuG trehalose ABC transporter, permease component 2 (ThuG)
thuK trehalose ABC transporter, ATPase component ThuK Ga0059261_3668 Ga0059261_3874
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase Ga0059261_1580
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) Ga0059261_1646 Ga0059261_1647
treP trehalose phosphorylase, inverting
trePP trehalose-6-phosphate phosphorylase
treS trehalose ABC transporter, substrate-binding comopnent TreS
treT trehalose ABC transporter, permease component 1 (TreT)
TRET1 facilitated trehalose transporter Tret1 Ga0059261_1777
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV Ga0059261_3668 Ga0059261_0341

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory